diff --git a/app/src/processing/app/Base.java b/app/src/processing/app/Base.java
index d45d9c638f2..95becc3b0b2 100644
--- a/app/src/processing/app/Base.java
+++ b/app/src/processing/app/Base.java
@@ -344,13 +344,15 @@ public Base(String[] args) throws Exception {
     PreferencesData.save();
 
     if (parser.isInstallBoard()) {
-      ContributionsIndexer indexer = new ContributionsIndexer(BaseNoGui.getSettingsFolder(), BaseNoGui.getPlatform(), new GPGDetachedSignatureVerifier());
+      ContributionsIndexer indexer = new ContributionsIndexer(
+          BaseNoGui.getSettingsFolder(), BaseNoGui.getHardwareFolder(),
+          BaseNoGui.getPlatform(), new GPGDetachedSignatureVerifier());
       ProgressListener progressListener = new ConsoleProgressListener();
 
       List<String> downloadedPackageIndexFiles = contributionInstaller.updateIndex(progressListener);
       contributionInstaller.deleteUnknownFiles(downloadedPackageIndexFiles);
       indexer.parseIndex();
-      indexer.syncWithFilesystem(BaseNoGui.getHardwareFolder());
+      indexer.syncWithFilesystem();
 
       String[] boardToInstallParts = parser.getBoardToInstall().split(":");
 
diff --git a/arduino-core/src/cc/arduino/Constants.java b/arduino-core/src/cc/arduino/Constants.java
index 3c90abe7da6..80349d82dae 100644
--- a/arduino-core/src/cc/arduino/Constants.java
+++ b/arduino-core/src/cc/arduino/Constants.java
@@ -39,6 +39,7 @@ public class Constants {
   public static final String PREF_CONTRIBUTIONS_TRUST_ALL = "contributions.trust.all";
 
   public static final String DEFAULT_INDEX_FILE_NAME = "package_index.json";
+  public static final String BUNDLED_INDEX_FILE_NAME = "package_index_bundled.json";
   public static final List<String> PROTECTED_PACKAGE_NAMES = Arrays.asList("arduino", "Intel");
 
   public static final String LIBRARY_DEVELOPMENT_FLAG_FILE = ".development";
diff --git a/arduino-core/src/cc/arduino/contributions/packages/ContributionInstaller.java b/arduino-core/src/cc/arduino/contributions/packages/ContributionInstaller.java
index 47f895be638..bbf9fab9fe9 100644
--- a/arduino-core/src/cc/arduino/contributions/packages/ContributionInstaller.java
+++ b/arduino-core/src/cc/arduino/contributions/packages/ContributionInstaller.java
@@ -79,16 +79,15 @@ public synchronized List<String> install(ContributedPlatform contributedPlatform
     }
 
     // Do not download already installed tools
-    List<ContributedTool> tools = new LinkedList<>(contributedPlatform.getResolvedTools());
-    Iterator<ContributedTool> toolsIterator = tools.iterator();
-    while (toolsIterator.hasNext()) {
-      ContributedTool tool = toolsIterator.next();
+    List<ContributedTool> tools = new ArrayList<>();
+    for (ContributedTool tool : contributedPlatform.getResolvedTools()) {
       DownloadableContribution downloadable = tool.getDownloadableContribution(platform);
       if (downloadable == null) {
         throw new Exception(format(tr("Tool {0} is not available for your operating system."), tool.getName()));
       }
-      if (downloadable.isInstalled()) {
-        toolsIterator.remove();
+      // Download the tool if it's not installed or it's a built-in tool
+      if (!downloadable.isInstalled() || downloadable.isReadOnly()) {
+        tools.add(tool);
       }
     }
 
@@ -125,10 +124,10 @@ public synchronized List<String> install(ContributedPlatform contributedPlatform
 
     List<Map.Entry<ContributedToolReference, ContributedTool>> resolvedToolReferences = contributedPlatform.getResolvedToolReferences().entrySet()
       .stream()
-      .filter((entry) -> !entry.getValue().getDownloadableContribution(platform).isInstalled())
+      .filter((entry) -> !entry.getValue().getDownloadableContribution(platform).isInstalled()
+          || entry.getValue().getDownloadableContribution(platform).isReadOnly())
       .collect(Collectors.toList());
 
-
     int i = 1;
     for (Map.Entry<ContributedToolReference, ContributedTool> entry : resolvedToolReferences) {
       progress.setStatus(format(tr("Installing tools ({0}/{1})..."), i, resolvedToolReferences.size()));
@@ -249,11 +248,16 @@ public synchronized List<String> remove(ContributedPlatform contributedPlatform)
 
     // Check if the tools are no longer needed
     for (ContributedTool tool : contributedPlatform.getResolvedTools()) {
-      if (BaseNoGui.indexer.isContributedToolUsed(contributedPlatform, tool)) {
+      // Do not remove used tools
+      if (BaseNoGui.indexer.isContributedToolUsed(contributedPlatform, tool))
         continue;
-      }
 
+      // Do not remove built-in tools
       DownloadableContribution toolContrib = tool.getDownloadableContribution(platform);
+      if (toolContrib.isReadOnly())
+        continue;
+
+      // Ok, delete the tool
       File destFolder = toolContrib.getInstalledFolder();
       FileUtils.recursiveDelete(destFolder);
       toolContrib.setInstalled(false);
diff --git a/arduino-core/src/cc/arduino/contributions/packages/ContributionsIndex.java b/arduino-core/src/cc/arduino/contributions/packages/ContributionsIndex.java
index 6f9295f74d6..1ffc97d0229 100644
--- a/arduino-core/src/cc/arduino/contributions/packages/ContributionsIndex.java
+++ b/arduino-core/src/cc/arduino/contributions/packages/ContributionsIndex.java
@@ -141,8 +141,4 @@ public String toString() {
       res += pack + "\n";
     return res;
   }
-
-  public void setTrusted() {
-    getPackages().stream().forEach(pack -> pack.setTrusted(true));
-  }
 }
diff --git a/arduino-core/src/cc/arduino/contributions/packages/ContributionsIndexer.java b/arduino-core/src/cc/arduino/contributions/packages/ContributionsIndexer.java
index 5e8fb03ab95..f38d81e4c67 100644
--- a/arduino-core/src/cc/arduino/contributions/packages/ContributionsIndexer.java
+++ b/arduino-core/src/cc/arduino/contributions/packages/ContributionsIndexer.java
@@ -66,12 +66,14 @@ public class ContributionsIndexer {
   private final File packagesFolder;
   private final File stagingFolder;
   private final File preferencesFolder;
+  private final File builtInHardwareFolder;
   private final Platform platform;
   private final SignatureVerifier signatureVerifier;
   private ContributionsIndex index;
 
-  public ContributionsIndexer(File preferencesFolder, Platform platform, SignatureVerifier signatureVerifier) {
+  public ContributionsIndexer(File preferencesFolder, File builtInHardwareFolder, Platform platform, SignatureVerifier signatureVerifier) {
     this.preferencesFolder = preferencesFolder;
+    this.builtInHardwareFolder = builtInHardwareFolder;
     this.platform = platform;
     this.signatureVerifier = signatureVerifier;
     packagesFolder = new File(preferencesFolder, "packages");
@@ -79,13 +81,25 @@ public ContributionsIndexer(File preferencesFolder, Platform platform, Signature
   }
 
   public void parseIndex() throws Exception {
+    // Read bundled index...
+    File bundledIndexFile = new File(builtInHardwareFolder, Constants.BUNDLED_INDEX_FILE_NAME);
+    index = parseIndex(bundledIndexFile);
+
+    // ...and overlay the default index if present
     File defaultIndexFile = getIndexFile(Constants.DEFAULT_INDEX_FILE_NAME);
-    if (!PreferencesData.getBoolean("allow_insecure_packages") && !signatureVerifier.isSigned(defaultIndexFile)) {
-      throw new SignatureVerificationFailedException(Constants.DEFAULT_INDEX_FILE_NAME);
+    if (defaultIndexFile.exists()) {
+      // Check main index signature
+      if (!PreferencesData.getBoolean("allow_insecure_packages") && !signatureVerifier.isSigned(defaultIndexFile)) {
+        throw new SignatureVerificationFailedException(Constants.DEFAULT_INDEX_FILE_NAME);
+      }
+
+      mergeContributions(parseIndex(defaultIndexFile), defaultIndexFile);
     }
-    index = parseIndex(defaultIndexFile);
-    index.setTrusted();
 
+    // Set main and bundled indexes as trusted
+    index.getPackages().forEach(pack -> pack.setTrusted(true));
+
+    // Overlay 3rd party indexes
     File[] indexFiles = preferencesFolder.listFiles(new TestPackageIndexFilenameFilter(new PackageIndexFilenameFilter(Constants.DEFAULT_INDEX_FILE_NAME)));
 
     for (File indexFile : indexFiles) {
@@ -98,6 +112,7 @@ public void parseIndex() throws Exception {
       }
     }
 
+    // Fill tools and toolsDependency cross references
     List<ContributedPackage> packages = index.getPackages();
     Collection<ContributedPackage> packagesWithTools = packages.stream()
       .filter(input -> input.getTools() != null && !input.getTools().isEmpty())
@@ -188,32 +203,42 @@ private ContributionsIndex parseIndex(File indexFile) throws IOException {
     }
   }
 
-  public void syncWithFilesystem(File hardwareFolder) throws IOException {
-    syncBuiltInHardwareFolder(hardwareFolder);
+  public void syncWithFilesystem() throws IOException {
+    syncBuiltInHardware();
 
-    syncLocalPackagesFolder();
+    syncLocalPackages();
   }
 
-  private void syncBuiltInHardwareFolder(File hardwareFolder) throws IOException {
+  private void syncBuiltInHardware() throws IOException {
     if (index == null) {
       return;
     }
-    for (File folder : hardwareFolder.listFiles(ONLY_DIRS)) {
+    for (File folder : builtInHardwareFolder.listFiles(ONLY_DIRS)) {
       ContributedPackage pack = index.findPackage(folder.getName());
-      if (pack != null) {
-        syncBuiltInPackageWithFilesystem(pack, folder);
-
-        File toolsFolder = new File(hardwareFolder, "tools");
-        if (toolsFolder.isDirectory()) {
-          for (File toolFolder : toolsFolder.listFiles(ONLY_DIRS)) {
-            File builtInToolsMetadata = new File(toolFolder, "builtin_tools_versions.txt");
-            if (builtInToolsMetadata.isFile()) {
-              PreferencesMap toolsMetadata = new PreferencesMap(builtInToolsMetadata).subTree(pack.getName());
-              for (Map.Entry<String, String> toolMetadata : toolsMetadata.entrySet()) {
-                syncToolWithFilesystem(pack, toolFolder, toolMetadata.getKey(), toolMetadata.getValue());
-              }
-            }
-          }
+      if (pack == null)
+        continue;
+      syncBuiltInPackageWithFilesystem(pack, folder);
+
+      File toolsFolder = new File(builtInHardwareFolder, "tools");
+      if (!toolsFolder.isDirectory())
+        continue;
+
+      for (File toolFolder : toolsFolder.listFiles(ONLY_DIRS)) {
+
+        // builtin_tools_versions.txt contains tools versions in the format:
+        // "PACKAGER.TOOL_NAME=TOOL_VERSION"
+        // for example:
+        // "arduino.avrdude=6.0.1-arduino5"
+
+        File versionsFile = new File(toolFolder, "builtin_tools_versions.txt");
+        if (!versionsFile.isFile())
+          continue;
+        PreferencesMap toolsVersion = new PreferencesMap(versionsFile).subTree(pack.getName());
+        for (String name : toolsVersion.keySet()) {
+          String version = toolsVersion.get(name);
+          DownloadableContribution tool = syncToolWithFilesystem(pack, toolFolder, name, version);
+          if (tool != null)
+            tool.setReadOnly(true);
         }
       }
     }
@@ -231,7 +256,7 @@ private void syncBuiltInPackageWithFilesystem(ContributedPackage pack, File hard
     }
   }
 
-  private void syncLocalPackagesFolder() {
+  private void syncLocalPackages() {
     if (!packagesFolder.isDirectory()) {
       return;
     }
@@ -272,21 +297,23 @@ private void syncPackageWithFilesystem(ContributedPackage pack, File root) {
     }
   }
 
-  private void syncToolWithFilesystem(ContributedPackage pack, File installationFolder, String toolName, String version) {
+  private DownloadableContribution syncToolWithFilesystem(ContributedPackage pack, File installationFolder, String toolName, String version) {
     ContributedTool tool = pack.findTool(toolName, version);
     if (tool == null) {
       tool = pack.findResolvedTool(toolName, version);
     }
     if (tool == null) {
-      return;
+      return null;
     }
     DownloadableContribution contrib = tool.getDownloadableContribution(platform);
     if (contrib == null) {
       System.err.println(tool + " seems to have no downloadable contributions for your operating system, but it is installed in\n" + installationFolder);
-      return;
+      return null;
     }
     contrib.setInstalled(true);
     contrib.setInstalledFolder(installationFolder);
+    contrib.setReadOnly(false);
+    return contrib;
   }
 
   private ContributedPlatform syncHardwareWithFilesystem(ContributedPackage pack, File installationFolder, String architecture, String version) {
@@ -350,7 +377,7 @@ public boolean isContributedToolUsed(ContributedPlatform platformToIgnore, Contr
         if (platformToIgnore.equals(platform)) {
           continue;
         }
-        if (!platform.isInstalled()) {
+        if (!platform.isInstalled() || platform.isReadOnly()) {
           continue;
         }
         for (ContributedTool requiredTool : platform.getResolvedTools()) {
diff --git a/arduino-core/src/processing/app/BaseNoGui.java b/arduino-core/src/processing/app/BaseNoGui.java
index 43b99aff8b8..b160605c51e 100644
--- a/arduino-core/src/processing/app/BaseNoGui.java
+++ b/arduino-core/src/processing/app/BaseNoGui.java
@@ -608,36 +608,19 @@ static public void initLogger() {
   }
 
   static public void initPackages() throws Exception {
-    indexer = new ContributionsIndexer(BaseNoGui.getSettingsFolder(), BaseNoGui.getPlatform(), new GPGDetachedSignatureVerifier());
-    File indexFile = indexer.getIndexFile("package_index.json");
-    File defaultPackageJsonFile = new File(getContentFile("dist"), "package_index.json");
-    if (!indexFile.isFile() || (defaultPackageJsonFile.isFile() && defaultPackageJsonFile.lastModified() > indexFile.lastModified())) {
-      FileUtils.copyFile(defaultPackageJsonFile, indexFile);
-    } else if (!indexFile.isFile()) {
-      // Otherwise create an empty packages index
-      FileOutputStream out = null;
-      try {
-        out = new FileOutputStream(indexFile);
-        out.write("{ \"packages\" : [ ] }".getBytes());
-      } finally {
-        IOUtils.closeQuietly(out);
-      }
-    }
-
-    File indexSignatureFile = indexer.getIndexFile("package_index.json.sig");
-    File defaultPackageJsonSignatureFile = new File(getContentFile("dist"), "package_index.json.sig");
-    if (!indexSignatureFile.isFile() || (defaultPackageJsonSignatureFile.isFile() && defaultPackageJsonSignatureFile.lastModified() > indexSignatureFile.lastModified())) {
-      FileUtils.copyFile(defaultPackageJsonSignatureFile, indexSignatureFile);
-    }
+    indexer = new ContributionsIndexer(getSettingsFolder(), getHardwareFolder(), getPlatform(),
+        new GPGDetachedSignatureVerifier());
 
     try {
       indexer.parseIndex();
     } catch (JsonProcessingException | SignatureVerificationFailedException e) {
+      File indexFile = indexer.getIndexFile(Constants.DEFAULT_INDEX_FILE_NAME);
+      File indexSignatureFile = indexer.getIndexFile(Constants.DEFAULT_INDEX_FILE_NAME + ".sig");
       FileUtils.deleteIfExists(indexFile);
       FileUtils.deleteIfExists(indexSignatureFile);
       throw e;
     }
-    indexer.syncWithFilesystem(getHardwareFolder());
+    indexer.syncWithFilesystem();
 
     packages = new LinkedHashMap<String, TargetPackage>();
     loadHardware(getHardwareFolder());
diff --git a/build/build.xml b/build/build.xml
index 4723bcda7ad..83c09fda806 100644
--- a/build/build.xml
+++ b/build/build.xml
@@ -10,7 +10,6 @@
 
   <!-- Main url for boards and libraries repository -->
   <property name="library_index_url" value="http://downloads.arduino.cc/libraries/library_index.json" />
-  <property name="package_index_url" value="http://downloads.arduino.cc/packages/package_index.json" />
 
   <!-- Sets properties for macosx/windows/linux depending on current system -->
   <condition property="platform" value="macosx-old">
@@ -92,7 +91,6 @@
   <property name="ARDUINO-BUILDER-VERSION" value="1.3.20" />
   <property name="LIBLISTSERIAL-VERSION" value="1.1.4" />
   <property name="AVRGCC-VERSION" value="4.9.2-atmel3.5.3-arduino2" />
-  <property name="AVRDUDE-VERSION" value="6.3.0-arduino2" />
 
   <!-- Libraries required for running arduino -->
   <fileset dir=".." id="runtime.jars">
@@ -275,7 +273,7 @@
     </loadfile>
 
     <!-- figure out the latest AVR core version number in package_index.json -->
-    <loadfile srcfile="${staging_folder}/work/${staging_hardware_folder}/../dist/package_index.json" property="revision.avr.index">
+    <loadfile srcfile="${staging_folder}/work/${staging_hardware_folder}/package_index_bundled.json" property="revision.avr.index">
       <filterchain>
         <tokenfilter>
           <linetokenizer />
@@ -287,7 +285,7 @@
     </loadfile>
 
     <echo message="AVR Arduino core version in platform.txt is: ${revision.avr.platform}" />
-    <echo message="                    latest in index.json is: ${revision.avr.index}" />
+    <echo message="    latest in package_index_bundled.json is: ${revision.avr.index}" />
     <condition property="revision.avr.ok">
       <or>
         <!-- fail build if -Drevision.check=enforce is set -->
@@ -296,8 +294,8 @@
       </or>
     </condition>
     <fail unless="revision.avr.ok">
-      Mismatching versions for bundled AVR core and package_index.json.
-      Please check your platform.txt and package_index.json.
+      Mismatching versions for bundled AVR core and package_index_bundled.json.
+      Please check your platform.txt and package_index_bundled.json.
     </fail>
 
     <!-- figure out the IDE version number -->
@@ -494,8 +492,8 @@
       <param name="unpack_target" value="untar"/>
       <param name="gcc_archive_file" value="avr-gcc-${AVRGCC-VERSION}-i386-apple-darwin11.tar.bz2"/>
       <param name="gcc_version" value="${AVRGCC-VERSION}"/>
-      <param name="avrdude_archive_file" value="avrdude-${AVRDUDE-VERSION}-i386-apple-darwin11.tar.bz2"/>
-      <param name="avrdude_version" value="${AVRDUDE-VERSION}"/>
+      <param name="avrdude_archive_file" value="avrdude-6.0.1-arduino5-r2-i386-apple-darwin11.tar.bz2"/>
+      <param name="avrdude_version" value="6.0.1-arduino5"/>
     </antcall>
 
     <chmod perm="+x">
@@ -719,8 +717,8 @@
       <param name="unpack_target" value="untar"/>
       <param name="gcc_archive_file" value="avr-gcc-${AVRGCC-VERSION}-armhf-pc-linux-gnu.tar.bz2"/>
       <param name="gcc_version" value="${AVRGCC-VERSION}"/>
-      <param name="avrdude_archive_file" value="avrdude-${AVRDUDE-VERSION}-armhf-pc-linux-gnu.tar.bz2"/>
-      <param name="avrdude_version" value="${AVRDUDE-VERSION}"/>
+      <param name="avrdude_archive_file" value="avrdude-6.0.1-arduino5-armhf-pc-linux-gnu-glibc2.13.tar.bz2"/>
+      <param name="avrdude_version" value="6.0.1-arduino5"/>
     </antcall>
 
     <antcall target="package-library-index-json-bundle"/>
@@ -751,8 +749,8 @@
       <param name="unpack_target" value="untar"/>
       <param name="gcc_archive_file" value="avr-gcc-${AVRGCC-VERSION}-i686-pc-linux-gnu.tar.bz2"/>
       <param name="gcc_version" value="${AVRGCC-VERSION}"/>
-      <param name="avrdude_archive_file" value="avrdude-${AVRDUDE-VERSION}-i686-pc-linux-gnu.tar.bz2"/>
-      <param name="avrdude_version" value="${AVRDUDE-VERSION}"/>
+      <param name="avrdude_archive_file" value="avrdude-6.0.1-arduino5-i686-pc-linux-gnu.tar.bz2"/>
+      <param name="avrdude_version" value="6.0.1-arduino5"/>
     </antcall>
 
     <antcall target="package-library-index-json-bundle"/>
@@ -783,8 +781,8 @@
       <param name="unpack_target" value="untar"/>
       <param name="gcc_archive_file" value="avr-gcc-${AVRGCC-VERSION}-x86_64-pc-linux-gnu.tar.bz2"/>
       <param name="gcc_version" value="${AVRGCC-VERSION}"/>
-      <param name="avrdude_archive_file" value="avrdude-${AVRDUDE-VERSION}-x86_64-pc-linux-gnu.tar.bz2"/>
-      <param name="avrdude_version" value="${AVRDUDE-VERSION}"/>
+      <param name="avrdude_archive_file" value="avrdude-6.0.1-arduino5-x86_64-pc-linux-gnu.tar.bz2"/>
+      <param name="avrdude_version" value="6.0.1-arduino5"/>
     </antcall>
 
     <antcall target="package-library-index-json-bundle"/>
@@ -1071,8 +1069,8 @@
       <param name="unpack_target" value="unzip"/>
       <param name="gcc_archive_file" value="avr-gcc-${AVRGCC-VERSION}-i686-mingw32.zip"/>
       <param name="gcc_version" value="${AVRGCC-VERSION}"/>
-      <param name="avrdude_archive_file" value="avrdude-${AVRDUDE-VERSION}-i686-w64-mingw32.zip"/>
-      <param name="avrdude_version" value="${AVRDUDE-VERSION}"/>
+      <param name="avrdude_archive_file" value="avrdude-6.0.1-arduino5-i686-mingw32.zip"/>
+      <param name="avrdude_version" value="6.0.1-arduino5"/>
     </antcall>
 
     <antcall target="package-library-index-json-bundle"/>
@@ -1161,26 +1159,18 @@
     </antcall>
 
     <move file="${staging_folder}/work/${staging_hardware_folder}/tmp/gcc/avr" tofile="${staging_folder}/work/${staging_hardware_folder}/tools/avr"/>
-    <move file="${staging_folder}/work/${staging_hardware_folder}/tmp/avrdude/avrdude" tofile="${staging_folder}/work/${staging_hardware_folder}/tools/avr"/>
+    <move file="${staging_folder}/work/${staging_hardware_folder}/tmp/avrdude/avrdude-6.0.1" tofile="${staging_folder}/work/${staging_hardware_folder}/tools/avr"/>
+    <antcall target="macosx-fix-bundled-toolchain-missing-symlinks"/>
 
     <echo append="true" file="${staging_folder}/work/${staging_hardware_folder}/tools/avr/builtin_tools_versions.txt" message="arduino.avrdude=${avrdude_version}${line.separator}"/>
     <echo append="true" file="${staging_folder}/work/${staging_hardware_folder}/tools/avr/builtin_tools_versions.txt" message="arduino.avr-gcc=${gcc_version}${line.separator}"/>
   </target>
 
   <target name="package-library-index-json-bundle">
-    <mkdir dir="${staging_folder}/work/${staging_hardware_folder}/../dist/"/>
-
-    <get src="${package_index_url}.gz"
-         dest="${staging_folder}/work/${staging_hardware_folder}/../dist/package_index.json.gz"
-         verbose="true" skipexisting="false" />
-    <gunzip src ="${staging_folder}/work/${staging_hardware_folder}/../dist/package_index.json.gz"
-            dest="${staging_folder}/work/${staging_hardware_folder}/../dist/"/>
-    <delete file="${staging_folder}/work/${staging_hardware_folder}/../dist/package_index.json.gz"/>
-
-    <get src="${package_index_url}.sig"
-         dest="${staging_folder}/work/${staging_hardware_folder}/../dist/package_index.json.sig"
-         verbose="true" skipexisting="false" />
+    <mkdir dir="${staging_folder}/work/${staging_hardware_folder}"/>
+    <copy file="../hardware/package_index_bundled.json" tofile="${staging_folder}/work/${staging_hardware_folder}/package_index_bundled.json"/>
 
+    <mkdir dir="${staging_folder}/work/${staging_hardware_folder}/../dist/"/>
     <get src="${library_index_url}.gz"
          dest="${staging_folder}/work/${staging_hardware_folder}/../dist/library_index.json.gz"
          verbose="true" skipexisting="false" />
@@ -1191,6 +1181,17 @@
     <delete dir="${staging_folder}/work/${staging_hardware_folder}/tmp"/>
   </target>
 
+  <target name="macosx-fix-bundled-toolchain-missing-symlinks" if="macosx">
+    <exec executable="mv" failonerror="true">
+      <arg value="${staging_folder}/work/${staging_hardware_folder}/tmp/avrdude/avrdude-6.0.1/lib/libusb.dylib"/>
+      <arg value="${staging_folder}/work/${staging_hardware_folder}/tools/avr/lib/"/>
+    </exec>
+    <exec executable="mv" failonerror="true">
+      <arg value="${staging_folder}/work/${staging_hardware_folder}/tmp/avrdude/avrdude-6.0.1/lib/libusb-1.0.dylib"/>
+      <arg value="${staging_folder}/work/${staging_hardware_folder}/tools/avr/lib/"/>
+    </exec>
+  </target>
+
   <target name="generate-hourly-build-txt" if="hourly">
     <echo file="${staging_folder}/work/${staging_hardware_folder}/../lib/hourlyBuild.txt">${BUILD_DATE}</echo>
   </target>
diff --git a/build/linux/avrdude-6.0.1-arduino5-armhf-pc-linux-gnu-glibc2.13.tar.bz2.sha b/build/linux/avrdude-6.0.1-arduino5-armhf-pc-linux-gnu-glibc2.13.tar.bz2.sha
new file mode 100644
index 00000000000..6d87ebcafe9
--- /dev/null
+++ b/build/linux/avrdude-6.0.1-arduino5-armhf-pc-linux-gnu-glibc2.13.tar.bz2.sha
@@ -0,0 +1 @@
+b5968416647e79f5c395bf2a9ba000127dacc9da
diff --git a/build/linux/avrdude-6.0.1-arduino5-i686-pc-linux-gnu.tar.bz2.sha b/build/linux/avrdude-6.0.1-arduino5-i686-pc-linux-gnu.tar.bz2.sha
new file mode 100644
index 00000000000..0bc23f68811
--- /dev/null
+++ b/build/linux/avrdude-6.0.1-arduino5-i686-pc-linux-gnu.tar.bz2.sha
@@ -0,0 +1 @@
+cf859c679713cae2f1b9089d797d211dd84fe658
diff --git a/build/linux/avrdude-6.0.1-arduino5-x86_64-pc-linux-gnu.tar.bz2.sha b/build/linux/avrdude-6.0.1-arduino5-x86_64-pc-linux-gnu.tar.bz2.sha
new file mode 100644
index 00000000000..e4b0302e0fa
--- /dev/null
+++ b/build/linux/avrdude-6.0.1-arduino5-x86_64-pc-linux-gnu.tar.bz2.sha
@@ -0,0 +1 @@
+cfc52036f532c3a7050f6d4ec7645d060800aa39
diff --git a/build/linux/avrdude-6.3.0-arduino2-armhf-pc-linux-gnu.tar.bz2.sha b/build/linux/avrdude-6.3.0-arduino2-armhf-pc-linux-gnu.tar.bz2.sha
deleted file mode 100644
index 389ab1832ad..00000000000
--- a/build/linux/avrdude-6.3.0-arduino2-armhf-pc-linux-gnu.tar.bz2.sha
+++ /dev/null
@@ -1 +0,0 @@
-a074c17e2013942e3e081fe03875c9d5701a0922
diff --git a/build/linux/avrdude-6.3.0-arduino2-i686-pc-linux-gnu.tar.bz2.sha b/build/linux/avrdude-6.3.0-arduino2-i686-pc-linux-gnu.tar.bz2.sha
deleted file mode 100644
index 844fb6a27cc..00000000000
--- a/build/linux/avrdude-6.3.0-arduino2-i686-pc-linux-gnu.tar.bz2.sha
+++ /dev/null
@@ -1 +0,0 @@
-e9ce49f5e5c7d0d2eabd9405ca6160b70cd52645
diff --git a/build/linux/avrdude-6.3.0-arduino2-x86_64-pc-linux-gnu.tar.bz2.sha b/build/linux/avrdude-6.3.0-arduino2-x86_64-pc-linux-gnu.tar.bz2.sha
deleted file mode 100644
index 1104a38421e..00000000000
--- a/build/linux/avrdude-6.3.0-arduino2-x86_64-pc-linux-gnu.tar.bz2.sha
+++ /dev/null
@@ -1 +0,0 @@
-3ba4c2660f8a8c40ba3902ab8a158aa3e1b91764
diff --git a/build/macosx/avrdude-6.0.1-arduino5-r2-i386-apple-darwin11.tar.bz2.sha b/build/macosx/avrdude-6.0.1-arduino5-r2-i386-apple-darwin11.tar.bz2.sha
new file mode 100644
index 00000000000..3b1625eee60
--- /dev/null
+++ b/build/macosx/avrdude-6.0.1-arduino5-r2-i386-apple-darwin11.tar.bz2.sha
@@ -0,0 +1 @@
+52afce6cbe1cc1021bca1234cf25b298350f97dd
diff --git a/build/macosx/avrdude-6.3.0-arduino2-i386-apple-darwin11.tar.bz2.sha b/build/macosx/avrdude-6.3.0-arduino2-i386-apple-darwin11.tar.bz2.sha
deleted file mode 100644
index edb160cf3ea..00000000000
--- a/build/macosx/avrdude-6.3.0-arduino2-i386-apple-darwin11.tar.bz2.sha
+++ /dev/null
@@ -1 +0,0 @@
-39a1940fbb4a25af5316d9a6bde99b6a29585e37
diff --git a/build/shared/revisions.txt b/build/shared/revisions.txt
index 304f7ac41b3..96b272f85cf 100644
--- a/build/shared/revisions.txt
+++ b/build/shared/revisions.txt
@@ -4,6 +4,8 @@ ARDUINO 1.6.11
 * Fixed a serious bug that prevented some 3rd party boards, installed through external index.json URL, to work correctly.
 * builder: fixed regression about inclusion of files in subfolders of the sketch
   (see https://github.com/arduino/Arduino/issues/5186 for details)
+* avrdude: reverted to version 6.0.1, until all discovered regressions are solved
+  (see https://github.com/arduino/Arduino/issues?q=is%3Aissue+is%3Aopen+label%3A%22Component%3A+Avrdude+6.3%22 for details)
 
 ARDUINO 1.6.10 - 2016.07.26
 
diff --git a/build/windows/avrdude-6.0.1-arduino5-i686-mingw32.zip.sha b/build/windows/avrdude-6.0.1-arduino5-i686-mingw32.zip.sha
new file mode 100644
index 00000000000..e55aa9d558b
--- /dev/null
+++ b/build/windows/avrdude-6.0.1-arduino5-i686-mingw32.zip.sha
@@ -0,0 +1 @@
+bad246afeb0b9bcbe623a29cb204127f901102cf
diff --git a/hardware/arduino/avr/platform.txt b/hardware/arduino/avr/platform.txt
index 83cf12b2f84..0738d798113 100644
--- a/hardware/arduino/avr/platform.txt
+++ b/hardware/arduino/avr/platform.txt
@@ -6,7 +6,7 @@
 # https://github.com/arduino/Arduino/wiki/Arduino-IDE-1.5-3rd-party-Hardware-specification
 
 name=Arduino AVR Boards
-version=1.6.12
+version=1.6.13
 
 # AVR compile variables
 # ---------------------
diff --git a/hardware/package_index_bundled.json b/hardware/package_index_bundled.json
new file mode 100644
index 00000000000..4e301a285aa
--- /dev/null
+++ b/hardware/package_index_bundled.json
@@ -0,0 +1,146 @@
+{
+  "packages": [
+    {
+      "name": "arduino",
+      "maintainer": "Arduino",
+      "websiteURL": "http://www.arduino.cc/",
+      "email": "packages@arduino.cc",
+      "help": {
+        "online": "http://www.arduino.cc/en/Reference/HomePage"
+      },
+      "platforms": [
+        {
+          "name": "Arduino AVR Boards",
+          "architecture": "avr",
+          "version": "1.6.13",
+          "category": "Arduino",
+          "help": {
+            "online": "http://www.arduino.cc/en/Reference/HomePage"
+          },
+          "url": "http://downloads.arduino.cc/cores/avr-1.6.13.tar.bz2",
+          "archiveFileName": "avr-1.6.13.tar.bz2",
+          "checksum": "SHA-256:617f458dd3507072b9a6f9fdc78888c66aa420a2fb081c4c1556598a2d69d643",
+          "size": "4993644",
+          "boards": [
+            {"name": "Arduino Yún"},
+            {"name": "Arduino/Genuino Uno"},
+            {"name": "Arduino Diecimila"},
+            {"name": "Arduino Nano"},
+            {"name": "Arduino/Genuino Mega"},
+            {"name": "Arduino MegaADK"},
+            {"name": "Arduino Leonardo"},
+            {"name": "Arduino/Genuino Micro"},
+            {"name": "Arduino Esplora"},
+            {"name": "Arduino Mini"},
+            {"name": "Arduino Ethernet"},
+            {"name": "Arduino Fio"},
+            {"name": "Arduino BT"},
+            {"name": "Arduino LilyPadUSB"},
+            {"name": "Arduino Lilypad"},
+            {"name": "Arduino Pro"},
+            {"name": "Arduino ATMegaNG"},
+            {"name": "Arduino Robot Control"},
+            {"name": "Arduino Robot Motor"},
+            {"name": "Arduino Gemma"}
+          ],
+          "toolsDependencies": [
+            {
+              "packager": "arduino",
+              "name": "avr-gcc",
+              "version": "4.9.2-atmel3.5.3-arduino2"
+            },
+            {
+              "packager": "arduino",
+              "name": "avrdude",
+              "version": "6.0.1-arduino5"
+            }
+          ]
+        }
+      ],
+      "tools": [
+        {
+          "name": "avrdude",
+          "version": "6.0.1-arduino5",
+          "systems": [
+            {
+              "size": "267095",
+              "checksum": "SHA-256:23ea1341dbc117ec067f2eb1a498ad2bdd7d11fff0143c00b2e018c39804f6b4",
+              "host": "arm-linux-gnueabihf",
+              "archiveFileName": "avrdude-6.0.1-arduino5-armhf-pc-linux-gnu.tar.bz2",
+              "url": "http://downloads.arduino.cc/tools/avrdude-6.0.1-arduino5-armhf-pc-linux-gnu.tar.bz2"
+            },
+            {
+              "size": "264894",
+              "checksum": "SHA-256:41af8d3b0a586853c8317b4fb5163ca0db594a1870ddf680fd988c42166fc3e5",
+              "host": "i386-apple-darwin11",
+              "archiveFileName": "avrdude-6.0.1-arduino5-i386-apple-darwin11.tar.bz2",
+              "url": "http://downloads.arduino.cc/tools/avrdude-6.0.1-arduino5-i386-apple-darwin11.tar.bz2"
+            },
+            {
+              "size": "292629",
+              "checksum": "SHA-256:d826cca7383461f7e8adde686372cf900e9cb3afd639555cf2d6c645b283a476",
+              "host": "x86_64-linux-gnu",
+              "archiveFileName": "avrdude-6.0.1-arduino5-x86_64-pc-linux-gnu.tar.bz2",
+              "url": "http://downloads.arduino.cc/tools/avrdude-6.0.1-arduino5-x86_64-pc-linux-gnu.tar.bz2"
+            },
+            {
+              "size": "283121",
+              "checksum": "SHA-256:5933d66927bce46ababa9b68a8b7f1d53f68c4f3ff7a5ce4b85d7cf4e6c6bfee",
+              "host": "i686-linux-gnu",
+              "archiveFileName": "avrdude-6.0.1-arduino5-i686-pc-linux-gnu.tar.bz2",
+              "url": "http://downloads.arduino.cc/tools/avrdude-6.0.1-arduino5-i686-pc-linux-gnu.tar.bz2"
+            },
+            {
+              "size": "241634",
+              "checksum": "SHA-256:41f667f1f6a0ab8df46b4ffacd023176dcdef331d6db3b74bddd37d18cca0a44",
+              "host": "i686-mingw32",
+              "archiveFileName": "avrdude-6.0.1-arduino5-i686-mingw32.zip",
+              "url": "http://downloads.arduino.cc/tools/avrdude-6.0.1-arduino5-i686-mingw32.zip"
+            }
+          ]
+        },
+        {
+          "name": "avr-gcc",
+          "version": "4.9.2-atmel3.5.3-arduino2",
+          "systems": [
+            {
+              "size": "27400889",
+              "checksum": "SHA-256:77f300d519bc6b9a25df17b36cb303218e9a258c059b2f6bff8f71a0d8f96821",
+              "host": "arm-linux-gnueabihf",
+              "archiveFileName": "avr-gcc-4.9.2-atmel3.5.3-arduino2-armhf-pc-linux-gnu.tar.bz2",
+              "url": "http://downloads.arduino.cc/tools/avr-gcc-4.9.2-atmel3.5.3-arduino2-armhf-pc-linux-gnu.tar.bz2"
+            },
+            {
+              "size": "27048070",
+              "checksum": "SHA-256:311258af188defe24a4b341e4e1f4dc93ca6c80516d3e3b55a2fc07a7050248b",
+              "host": "i386-apple-darwin11",
+              "archiveFileName": "avr-gcc-4.9.2-atmel3.5.3-arduino2-i386-apple-darwin11.tar.bz2",
+              "url": "http://downloads.arduino.cc/tools/avr-gcc-4.9.2-atmel3.5.3-arduino2-i386-apple-darwin11.tar.bz2"
+            },
+            {
+              "size": "43847945",
+              "checksum": "SHA-256:f8e6ede8746c70be01ec79a30803277cd94360cc5b2e104762da0fbcf536fcc6",
+              "host": "i686-mingw32",
+              "archiveFileName": "avr-gcc-4.9.2-atmel3.5.3-arduino2-i686-mingw32.zip",
+              "url": "http://downloads.arduino.cc/tools/avr-gcc-4.9.2-atmel3.5.3-arduino2-i686-mingw32.zip"
+            },
+            {
+              "size": "29292729",
+              "checksum": "SHA-256:f108951e7c4dc90926d1fc76cc27549f6ea63c702a2bb7ff39647a19ae86ec68",
+              "host": "i686-linux-gnu",
+              "archiveFileName": "avr-gcc-4.9.2-atmel3.5.3-arduino2-i686-pc-linux-gnu.tar.bz2",
+              "url": "http://downloads.arduino.cc/tools/avr-gcc-4.9.2-atmel3.5.3-arduino2-i686-pc-linux-gnu.tar.bz2"
+            },
+            {
+              "size": "29882960",
+              "checksum": "SHA-256:3903a6d1bb9fdd91727e504b5993d5501f119bcb7f99f7aee98a2101e5629188",
+              "host": "x86_64-linux-gnu",
+              "archiveFileName": "avr-gcc-4.9.2-atmel3.5.3-arduino2-x86_64-pc-linux-gnu.tar.bz2",
+              "url": "http://downloads.arduino.cc/tools/avr-gcc-4.9.2-atmel3.5.3-arduino2-x86_64-pc-linux-gnu.tar.bz2"
+            }
+          ]
+        }
+      ]
+    }
+  ]
+}